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Comparative genomic landscape of lower-grade glioma and glioblastoma.

Biomarkers for classifying and grading gliomas have been extensively explored, whereas populations in public databases were mostly Western/European. Based on public databases cannot accurately represent Chinese population. To identify molecular characteristics associated with clinical outcomes of lower-grade glioma (LGG) and glioblastoma (GBM) in the Chinese population, we performed whole-exome sequencing (WES) in 16 LGG and 35 GBM tumor tissues. TP53 (36/51), TERT (31/51), ATRX (16/51), EFGLAM (14/51), and IDH1 (13/51) were the most common genes harboring mutations. IDH1 mutation (c.G395A; p.R132H) was significantly enriched in LGG, whereas PCDHGA10 mutation (c.A265G; p.I89V) in GBM. IDH1-wildtype and PCDHGA10 mutation were significantly related to poor prognosis. IDH1 is an important biomarker in gliomas, whereas PCDHGA10 mutation has not been reported to correlate with gliomas. Different copy number variations (CNVs) and oncogenic signaling pathways were identified between LGG and GBM. Differential genomic landscapes between LGG and GBM were revealed in the Chinese population, and PCDHGA10, for the first time, was identified as the prognostic factor of gliomas. Our results might provide a basis for molecular classification and identification of diagnostic biomarkers and even potential therapeutic targets for gliomas.

Humans↗

Comparative proteome analysis of breast cancer and normal breast.

Breast cancer is a leading cause of death for women. The underlying molecular mechanism is still not well understood. In this study, two-dimensional gel electrophoresis combined with mass spectrometry was used to analyze changes in the proteome of infiltrating ductal carcinoma compared to normal breast tissue. Ten sets of two-dimensional gels per experimental condition were analyzed and more than 500 spots each were detected. This revealed 39 spots for which expression in breast cancer cells were reproducibly altered more than twofold compared to normal controls (p < 0.01). These spots represented 25 different proteins after identification using the database search after mass spectrometry, comprising cell defense proteins, enzymes involved in glycolytic energy metabolism and homeostasis, protein folding and structural proteins, proteins involved in cytoskeleton and cell motility, and proteins involved in other functions. In addition, 28 nondifferentially expressed proteins with different functions were also mapped and identified, which might help to establish a two-dimensional gel electrophoresis reference map of human breast cancer. Our study shows that proteomics offers a powerful methodology to detect the proteins that show different expression patterns in breast cancer tissue and may provide an accurate molecular classification. The differentially expressed proteins may be used as potential candidate markers for diagnostic purposes or for determination of tumor sensitivity to therapy. The functional implications of the identified proteins are discussed.

Biomarkers, Tumor↗

Combined analysis of COX-2 and p53 expressions reveals synergistic inverse correlations with microsatellite instability and CpG island methylator phenotype in colorectal cancer.

Cyclooxygenase-2 (COX-2) overexpression and mutations of p53 (a known COX-2 regulator) are inversely associated with microsatellite instability-high (MSI-H) and CpG island methylator phenotype (CIMP) characterized by extensive promoter methylation, is associated with MSI-H. However, no studies have comprehensively examined interrelations between COX-2, p53, MSI, and CIMP. Using MethyLight, we measured DNA methylation in five CIMP-specific gene promoters [CACNA1G, CDKN2A (p16/INK4A), CRABP1, MLH1, and NEUROG1] in relatively unbiased samples of 751 colorectal cancer cases obtained from two large prospective cohorts; 115 (15%) tumors were CIMP-high (> or = 4 of 5 methylated promoters), 251 (33%) were CIMP-low (1 to 3 methylated promoters), and the remaining 385 (51%) were CIMP-0 (no methylated promoters). CIMP-high tumors were much less frequent in COX-2+/p53+ tumors (4.6%) than in COX-2+/p53- tumors (19%; P < .0001), COX-2-/p53+ tumors (17%; P = .04), and COX-2-/p53- tumors (28%; P < .0001). In addition, COX-2+/p53+ tumors were significantly less common in MSI-H CIMP-high tumors (9.7%) than in non-MSI-H CIMP-low/CIMP-0 tumors (44-47%; P < .0001). In conclusion, COX-2 and p53 alterations were synergistically inversely correlated with both MSI-H and CIMP-high. Our data suggest that a combined analysis of COX-2 and p53 may be more useful for the molecular classification of colorectal cancer than either COX-2 or p53 analysis alone.

Cohort Studies↗

Risk-reducing mastectomy.

Breast cancer is a malignant proliferation of epithelial cells lining the ducts or lobules of the breast. Excluding skin cancer, breast cancer is the most common cancer in women. Only lung cancer accounts for more cancer deaths in women. Breast cancer may exist for a long period either as an invasive or noninvasive disease, but not as a nonmetastatic disease. Consequently, timely diagnosis and appropriate management are lifesaving. Approximately 10% of human breast cancers are linked to germline mutations, such BRCA1 and BRCA2. Correct staging of breast cancer patients is critical. It permits an accurate diagnosis, as well as in many cases, therapeutic decisions based largely on the TNM classification. Staging provides the most important prognostic variable. Second opinions of the staging of breast cancer by pathologic examination of the tissue is recommended. There are some variables in which the association with disease-free survival and overall survival seem clear and include estrogen and progesterone receptor cells, S-phase analysis using flow cytometry, histologic classification, molecular changes in the tumor as well as neovasculature semi-quantitative scoring systems. There are four objectives to risk-reducing mastectomy. First, risk-reducing mastectomy should reduce the incidence of breast cancer in high-risk women, for example, BRCA1 or BRCA2 carriers. It should reduce mortality from breast cancer in high-risk women. Moreover, it should have psychological benefits in relieving anxiety about developing breast cancer. Finally, there must be a balance in the reduction in risk against cosmetic outcome, with subsequent quality of life issues. Women should be offered risk reduction mastectomy only on the basis of a strict selection and management plan, like that used in Manchester protocol. This protocol involves a minimum of two sessions with a geneticist/oncologist, a session with a psychiatrist and two sessions with a plastic and reconstructive surgeon with the support of a breast care nurse. The surgical technique should aim at removing substantially all at-risk breast tissue. However, there is an obvious balance between reduction of cancer risk and cosmetic outcome. The surgical technique involves several operations to include the risk-reducing mastectomy as well as breast reconstructive procedures. Skin-sparing mastectomy represents a new surgical approach that allows a mastectomy, whereas preserving the natural skin envelope of the breast. Breast reconstruction will involve several operations, especially if the nipple areola complex is resected and is subsequently reconstructed. The contraindications to risk-reducing mastectomy include the following. The status of the family history or Munchausen's syndrome has not been confirmed. The risk-reducing mastectomy is not the women's own choice. The patient has a current psychiatric disorder including clinical depression, cancer phobia or body dysmorphic syndrome. If the co-morbidity outweighs the clinical benefits, surgery should not be undertaken. Finally, the patient must not have unrealistic expectations of the benefits of surgery. She must understand the subsequent risk-reducing mastectomy may significantly reduce, but not eliminate the risk of subsequent breast cancer.

Breast Neoplasms↗

Identification of differentially expressed genes from ovarian cancer cells by MICROMAX cDNA microarray system.

Using the MICROMAX cDNA microarray system, we were able to identify genes that are differentially overexpressed in ovarian cancer. A total of 30 putative genes, which are differentially overexpressed in ovarian cancer cell lines, were identified. The differential expression of some of these genes was further confirmed by real-time RT-PCR. Using this strategy, we have identified genes that either overexpress in all cancer cell lines or in only some cancer cell lines. Further characterization of these genes will allow them to be exploited in diagnosis, prognosis, anticancer therapy, and molecular classification of ovarian cancer.

Female↗

Indirect measurements of differential gene expression with cDNA microarrays.

The use of universal RNA reference sets is an increasingly common approach to molecular classification studies with cDNA microarrays. Here we evaluated the reliability of indirect measurements of fluorescence ratios with a common RNA reference as a means of identifying differentially expressed genes. Comparisons of direct and indirect measures of differential gene expression showed a strong overall correlation in fluorescence ratio measurements but also a high degree of false positives in our indirect measurements. These results indicated that the application of more stringent ratio filters may be required when assessing differential gene expression utilizing a common RNA reference in classification studies.

DNA, Complementary↗

The KEAP1-NFE2L2/NRF2 Axis in Non-Small Cell Lung Cancer Radioresistance: Redox Homeostasis and Emerging DNA Damage Response Mechanisms.

Radioresistance and local recurrence remain major barriers to effective radiotherapy in non-small cell lung cancer (NSCLC). Loss-of-function KEAP1 alterations or activating NFE2L2 alterations can stabilize NRF2, but do not alone establish sustained transcriptional activity or functional dependency. This focused narrative review evaluates clinical radiotherapy studies and mechanistically informative preclinical studies linking the KEAP1-NFE2L2/NRF2 axis to NSCLC radioresistance. We prioritized clinical studies reporting radiotherapy-specific outcomes and preclinical studies coupling NRF2-related molecular status or perturbation with radiation-response endpoints; contextual studies informed metabolic, DNA damage response (DDR), immune and normal-lung effects. Evidence most consistently supports NRF2-mediated redox protection through glutathione-dependent defense, cellular reducing capacity and antioxidant enzymes, limiting radiation-induced reactive oxygen species (ROS) accumulation and oxidative injury. Limited studies further suggest that NRF2 may affect DNA-damage signaling, checkpoint control and repair. The detailed RPA32-TOPBP1-ATR-CHK1 model is therefore considered proposed rather than established in NRF2-active NSCLC. Retrospective clinical studies associate pathogenic KEAP1/NFE2L2 alterations with impaired local control in some radiotherapy-treated cohorts, but do not justify treating genomic status, protein abundance, transcriptional activity and functional dependency as equivalent measures or demonstrate treatment-predictive value. NRF2-mediated normal-lung protection also constrains systemic inhibition. Prospective studies integrating molecular classification, radiation-response endpoints, local control and normal-tissue toxicity are required before biomarker-guided radiosensitization can be considered.

DNA damage response↗

Gene expression profiling as a diagnostic tool in acute myeloid leukemia.

The standard methods for establishing the diagnosis of acute leukemias are cytomorphology and cytochemistry in combination with multiparameter immunophenotyping. Cytogenetics, fluorescence in situ hybridization, and PCR-based assays add important information regarding biologically defined and prognostically relevant subgroups, and allow a comprehensive diagnosis of well-defined subentities. In the clinical setting, a better understanding of the clinical course of distinct, biologically defined disease subtypes is the basis for a selection of disease-specific therapeutic approaches. As knowledge of deregulated pathways in leukemia increases and accelerates the development of new therapeutics, a detailed and comprehensive diagnostic tool is required. Microarray technology, which quantifies gene expression intensities of thousands of genes in a single analysis, has the potential to become an essential tool for the molecular classification of leukemias. It may, therefore, be used as a routine method for diagnostic purposes in the near future. Furthermore, gene expression profiling may also lead to the detection of new biologically defined and clinically relevant subtypes in leukemia and guide therapeutic decision-making in the future.

Acute Disease↗

Matrix metalloproteinases as therapeutic targets in cancer.

Degradation of extracellular matrix is crucial for malignant tumor growth, invasion, metastasis and angiogenesis. Matrix metalloproteinases (MMPs) are a family of zinc-dependent neutral endopeptidases collectively capable of degrading essentially all matrix components. Elevated levels of distinct MMPs can be detected in tumor tissue or serum of patients with advanced cancer, and their role as prognostic indicators in cancer has been widely examined. In addition, therapeutic intervention in tumor growth and invasion based on inhibition of MMP activity is under intensive investigation and several MMP inhibitors (MMPIs) are in clinical cancer trials. Even though results of the first clinical trials in advanced cancer have been mostly disappointing, there are also positive results. Recent observations show, that certain MMPs limit tumor growth. Therefore, identification of proper MMPs for therapeutic intervention with array-based molecular classifications of tumors and targeting these with more specific MMPIs in combination with conventional chemotherapy is expected to provide a feasible approach for cancer therapy. MMPIs represent a totally different therapeutic modality from proven anti-cancer drugs and thus traditional approaches to evaluate drug efficiency cannot be used without modification. In this review, we discuss the current view on the feasibility of MMPs as targets for therapeutic intervention in cancer.

Animals↗

Reproducible research: a bioinformatics case study.

While scientific research and the methodologies involved have gone through substantial technological evolution the technology involved in the publication of the results of these endeavors has remained relatively stagnant. Publication is largely done in the same manner today as it was fifty years ago. Many journals have adopted electronic formats, however, their orientation and style is little different from a printed document. The documents tend to be static and take little advantage of computational resources that might be available. Recent work, Gentleman and Temple Lang (2003), suggests a methodology and basic infrastructure that can be used to publish documents in a substantially different way. Their approach is suitable for the publication of papers whose message relies on computation. Stated quite simply, Gentleman and Temple Lang (2003) propose a paradigm where documents are mixtures of code and text. Such documents may be self-contained or they may be a component of a compendium which provides the infrastructure needed to provide access to data and supporting software. These documents, or compendiums, can be processed in a number of different ways. One transformation will be to replace the code with its output -- thereby providing the familiar, but limited, static document. In this paper we apply these concepts to a seminal paper in bioinformatics, namely The Molecular Classification of Cancer, Golub et al (1999). The authors of that paper have generously provided data and other information that have allowed us to largely reproduce their results. Rather than reproduce this paper exactly we demonstrate that such a reproduction is possible and instead concentrate on demonstrating the usefulness of the compendium concept itself.

Journal Article↗

Classifying gene expression profiles from pairwise mRNA comparisons.

We present a new approach to molecular classification based on mRNA comparisons. Our method, referred to as the top-scoring pair(s) (TSP) classifier, is motivated by current technical and practical limitations in using gene expression microarray data for class prediction, for example to detect disease, identify tumors or predict treatment response. Accurate statistical inference from such data is difficult due to the small number of observations, typically tens, relative to the large number of genes, typically thousands. Moreover, conventional methods from machine learning lead to decisions which are usually very difficult to interpret in simple or biologically meaningful terms. In contrast, the TSP classifier provides decision rules which i) involve very few genes and only relative expression values (e.g., comparing the mRNA counts within a single pair of genes); ii) are both accurate and transparent; and iii) provide specific hypotheses for follow-up studies. In particular, the TSP classifier achieves prediction rates with standard cancer data that are as high as those of previous studies which use considerably more genes and complex procedures. Finally, the TSP classifier is parameter-free, thus avoiding the type of over-fitting and inflated estimates of performance that result when all aspects of learning a predictor are not properly cross-validated.

Journal Article↗

Mapping the de-implementation of traditional diagnostic tests in pediatric acute lymphoblastic leukemia.

INTRODUCTION: Advances in cancer diagnostics raise questions about when and how to de-implement traditional approaches; however, these processes remain poorly described. At St. Jude Children's Research Hospital (SJCRH), routine conventional cytogenetics for pediatric acute lymphoblastic leukemia (ALL) diagnosis was de-implemented in 2018 following adoption of clinical genomics. This study aimed to map this process to inform future diagnostic de-implementation initiatives. METHODS: Interviews were conducted with SJCRH staff involved or impacted by cytogenetics de-implementation. Data were analyzed using thematic and rapid qualitative analysis informed by the Consolidated Framework for Implementation Research. Member-checking was used to verify and refine process maps, which were subsequently reviewed by an external expert panel, representing diverse settings, through focus group discussions. RESULTS: Thirteen SJCRH clinicians participated. De-implementation was described as successful, with no negative impact on patient outcomes. Decision-making began with internal correlation studies that demonstrated superior diagnostic performance of clinical genomics. De-implementation was viewed as a natural evolution that improved molecular classification, resource allocation, and workflow efficiency. Perceived risks included loss of cytogenetics competency, delayed turnaround time, and career insecurity, all addressed institutionally. Lessons learned highlighted the importance of deliberate discussion about logic and evidence supporting de-implementation. Fifteen external experts offered suggestions to improve process map generalizability, highlighting institutional- and system-level considerations. CONCLUSION: De-implementation of cytogenetics in ALL in favor of clinical genomics was successful at SJCRH. This study offers an example of diagnostic de-implementation in cancer care and proposes a structured approach to guide future efforts. De-implementation should be considered alongside introduction of novel diagnostic approaches.

cancer diagnostics↗

Receptor tyrosine kinase signaling in gliomagenesis: pathobiology and therapeutic approaches.

Gliomas are a large collection of primary central nervous system tumors that arise from glia, astrocytes and oligodendrocytes or their precursors. They are graded on a scale of I to IV based on their degree of malignancy as judged by variable histological features. Genetic and biochemical evidences have proven that gliomagenesis involves a stepwise accumulation of genetic lesions affecting either signal transduction pathways activated by receptor tyrosine kinases (RTKs) or cell cycle growth arrest pathways. Many of these observed molecular alterations are now being used to compliment clinical diagnosis. Genetic alterations affecting RTK signaling results in the activation of several downstream pathways, such as the PI3-kinase/Akt and Ras/Raf/MEK/MAPK pathways, which provides a number of novel targets for glioma therapy. This article aims to present a broad understanding of the receptor tyrosine kinase signaling networks involved in gliomagenesis. Molecular classification of primary glial tumors and elucidation of cooperative interactions between different genetic lesions will eventually allow us to target distinct glioma subsets and will provide a more rational approach to adjuvant therapies for this refractory disease.

Brain Neoplasms↗

Is the evidence in favour of neoadjuvant chemotherapy in stage IIIA (N2) non-small cell lung cancer solid enough?

In stage IIIA (N2) non-small cell lung cancer, single modality therapy with either surgery or radiation is curative in very few cases. The rationale behind neoadjuvant chemotherapy lies in the eradication of micrometastatic disease, which is often present when ipsilateral mediastinal or subcarinal lymph nodes (N2) are involved. Several studies have addressed the feasibility and efficacy of preoperative chemotherapy followed by surgery. All of these induction chemotherapy trials have reported a high radiographic response rate, high resectability rate and improved survival in completely resected patients. The findings reported in three published randomized trials indicate that the survival rate of stage IIIA patients is better with induction chemotherapy plus surgical resection than with resection alone. Phase II trials using preoperative concurrent chemoradiotherapy have been tested with encouraging results. Combined modality treatment in locally advanced non-small cell lung cancer continues to evolve and is the subject of ongoing research. New chemotherapeutic agents should be integrated into the neoadjuvant setting to improve results. A better understanding of the biology of tumours could well help in the optimization of these new agents. No doubt, in the future, molecular classification of non-small cell lung cancer will provide a useful tool for making therapy-related decisions.

Antineoplastic Agents↗

Transcriptional gene expression profiles of colorectal adenoma, adenocarcinoma, and normal tissue examined by oligonucleotide arrays.

Using an oligonucleotide array containing sequences complementary to approximately 3200 full-length human cDNAs and 3400 expressed sequence tags (GeneChip, Affymetrix), mRNA expression patterns were probed in 18 colon adenocarcinomas and 4 adenomas. Paired normal tissue was available and analyzed for each of the tumors. Relatively few changes in transcript expression are associated with colon cancer. Nineteen transcripts (0.48% of those detected) had at least 4-10.5-fold higher mRNA expression in carcinoma compared with paired normal samples, whereas 47 transcripts (1.3% of those detected) had at least 4-38-fold or lower expression in the tumor tissue compared with the normal samples. Some of these differences were confirmed by reverse transcription-PCR. Many of these transcripts were already known to be abnormally expressed in neoplastic tissue in general, or colon cancer in particular, and several of these differences were also observed in premalignant adenoma samples. A two-way hierarchical clustering algorithm successfully distinguished adenoma from adenocarcinoma and normal tissue, generating a phylogenetic tree that appropriately represented the clinical relationship between the three tissue types included in the analysis. This supports the concept that genome-wide expression profiling may permit a molecular classification of solid tumors.

Adenocarcinoma↗

Profiling of cancer cells using protein microarrays: discovery of novel radiation-regulated proteins.

The advent of DNA microarray technology will likely have a major impact on the molecular classification and understanding of human cancer. Obtaining a global perspective of proteins expressed in cancer cells is considerably more challenging. Here we describe a microarray-based platform that can be used to measure protein levels and activities in a complex biological milieu such as a cellular lysate. Using a protein microarray made up of 1920 elements (146 distinct antibodies) we were able to monitor alterations of protein levels in LoVo colon carcinoma cells treated with ionizing radiation. The protein microarray approach revealed radiation-induced up-regulation of apoptotic regulators including p53, DNA fragmentation factor 40/caspase activated DNase, DNA fragmentation factor 45/inhibitor of caspase activated DNase, tumor necrosis factor-related apoptosis-inducing ligand, death receptor 5, decoy receptor 2, FLICE-like inhibitory protein, signal transducers and activators of transcription 1alpha, and uncoupling protein 2, among others. Consistent with this observation, an increased percentage of apoptosis was observed in irradiated LoVo cells. Interestingly, we also observed radiation-induced down-regulation of carcinoembryonic antigen, a prototypic cancer biomarker. Selected proteins assessed by microarray were validated by traditional immunoblotting. Taken together, our work suggests that protein/antibody microarrays will facilitate high-throughput proteomic studies of human cancer and carcinogenesis.

Antibodies, Neoplasm↗

Genetic subgroups of anaplastic astrocytomas correlate with patient age and survival.

Astrocytomas are brain tumors with variable responses to radiation and chemotherapy. Tumor grade and patient age are important prognostic factors but do not account for the variability in clinical outcome. We hypothesized that genetic subgroups play a role in the outcome of grade III astrocytomas and studied 80 grade III astrocytomas by comparative genomic hybridization. Some chromosomal aberrations (+7p/q, -9p, -10q, -13q, +19q) were related to aberrations that are frequent in grade IV astrocytoma, whereas others (+10p, -11q, +11p, -Xq) were more frequent in grade III astrocytoma. +7p, +19 and -4q were more frequent in tumors from older patients while -11p was more frequent in tumors from younger patients. Finally, gains of 7p and 7q were associated with shorter patient survival, independent of age. Our results indicate that genetic events underlie the well-known effects of age on survival in grade III astrocytoma and demonstrate the importance of molecular classification in astrocytic tumors.

Adolescent↗

beta-Lactamases: quality and resistance.

beta-Lactamase-mediated resistance to beta-lactam antibiotics is a feature of great clinical significance. beta-Lactamases are a diverse group of bacterial enzymes that vary in their abilities to hydrolyze beta-lactam antibiotics. beta-Lactamases possess an active site containing either a serine moiety or a zinc atom; serine beta-lactamases are currently of greater clinical prevalence. This review considers the molecular classification of beta-lactamases, the structure of the serine beta-lactamase active site and the mechanisms by which beta-lactamase production may become derepressed. The spread of beta-lactamases in the clinical setting and some important structural mutations that have extended the hydrolysis profiles of serine beta-lactamases are also discussed.

Journal Article↗